December 15, 2007

This afternoon, on the outskirts of Lima, in a mountain village a mile and a half above sea level, all 46 children and each of their teachers are wired. Their laptops came courtesy of the One Laptop Per Child (OLPC) project, and a quarter million other Peruvian children will soon be wired as well, as are children in other pilot programs in Abuja, Nigeria; Villa Cardal, Uruguay; Samkha village, Thailand; Porto Alegre, Brazil; and Khairat, India.

There are several things to say about this remarkable project, but first let me establish the basics. The OLPC laptops are small, power-efficient laptops built to withstand rugged conditions. Each has a microphone, a camera, a screen that can be viewed in bright daylight or in dark, a small amount of flash memory (no hard drive), and innovative wireless networking capabilities that I'll come back to in a minute.

They are open-source, run linux, and are produced, sold, and distributed by a non-profit academic group as a charitable enterprise -- not by a computer company. From what I can tell, the villages that receive them are poor, but children have clothing, access to clean water, limited electricity (the laptops can be charged from a wide range of voltages, solar panels, or a hand pull), and some educational infrastructure. Rather than sprinkle the laptops throughout the population of developing countries, OLPC is targeting individual villages and saturating them, so that every child in the village has his or her own personal computer to use at school and at home.

A number of criticisms have been leveled against the program, including that the money would be better spent on providing more teachers, and that the program seeks to destroy some natural harmony that exists between poor people and the land (for example, here). With regard to the latter, the ads for the give-one-get-one program, showing a black girl with a laptop perched on her head like a bucket of water, leaves itself particularly open to critique, implying as it does -- to me, anyway -- that the program is targeted to Africa (it's not) and that the recipients are supposed to swap basic resources for new technology and smile.

I'll come back to these two topics -- what you can learn from a computer that you don't learn from a teacher, and whether "living in harmony with nature" is a myth -- in a couple of posts down the road. Right now, though, I'd like to overlook the question of all the good that I think will come out of the project in the future... and look instead at some of the good that, perhaps, already has.

November 17, 2007

The Intergovernmental Panel on Climate Change (IPCC) has released its fourth report (summary here), which synthesizes for policymakers attending the forthcoming UN conference in Bali the three reports that it issued earlier this year as part of its Fourth Assessment Report. Some of its conclusions are that

climate change is "unequivocal", that humankind's emissions of greenhouse gases are more than 90% likely to be the main cause, and that impacts can be reduced at reasonable cost.

But climate change may also bring about "abrupt and irreversible impacts" such as glacial melting and extinction of species.

"Approximately 20-30% of species assessed so far are likely to be at increased risk of extinction if increases in global average temperature exceed 1.5-2.5C (relative to the 1980-1999 average)," the summary concludes.

Other potential impacts highlighted in the text include:

between 75m and 250m people are projected to have scarcer fresh water supplies than at present

yields from rain-fed agriculture could be halved

food security is likely to be further compromised in Africa

there will be widespread impacts on coral reefs

One problem with the IPPC consensus process is that it takes a great deal of time, and thus it is not clear whether the newest report takes into account the accelerated arctic melting seen this year. But it is clear that things are happening faster than anticipated, the BBC reports:

"If you look at the overall picture of impacts, both those occurring now and those projected for the future, they appear to be both larger and appearing earlier than we thought [in our 2001 report]," Martin Parry, co-chair of the impacts working group, told BBC News.

"Some of the changes that we previously projected for around 2020 or 2030 are occurring now, such as the Arctic melt and shifts in the locations of various species."

There are indications that projected increases in droughts are also happening earlier than expected, he said, though that was less certain.

Interestingly, the IPPC finds that absent human factors, the climate would have cooled over the last 50 years (due to volcanoes and solar changes); only models that simulate human effects produce warming over this period. Warming is greatest in the northern polar regions and then in the north temperate and tropical zones (with the exception of the ocean area influenced by the jet stream). It is least in the southern temperate zone and southern seas. Human influences are "very likely" to have led to sea level increases.

The IPPC consensus now exhibits greater confidence in projections about droughts, heatwaves and floods, and their adverse consequences, plus stronger evidence of adverse impacts now on vulnerable ecosystems, such as polar and high-mountain regions and coral reefs.

In the ffuture, as temperatures rise, Africa and Asia will be particularly hard hit, in part because they already face shortages of good water and areas of extreme drought. Overall dry areas will become drier, low-lying areas will be wetter, smaller islands will be imperiled. Arctic areas will be transformed. Climate and weather will become more extreme. The widely-held impression that North America will suffer the least seems to be somewhat true, although serious effects are anticipated in cities that already experience heat waves, as are water shortages in the West, significant variability in agricultural impacts, increased intensity of Atlantic hurricanes and stress on coastal areas generally.

Projected changes are accelerating, and will persist for a millenium even if changes are made, raising the specter of whether, and how soon, we are facing irreversible changes or a "tipping point." Most serious seems to be accelerating Arctic ice melting, as this could cause meters of sea level increases, beyond what the models anticipate. The Jet Stream looks safe to the end of the century, despite some slowing, which will help moderate rising temperatures in Europe. (In case you were wondering, Dubai's spectacular islands have been designed to withstand at least a half meter rise in sea level, which was the high end anticipated by the end of this century. Some projections are now for three times that.)

Dealing with climate change has costs, but so does failing to deal with climate change, given the near certainty of the trajectory of change. The report concludes that

There is high agreement and much evidence that all stabilisation levels can be achieved by deployment of a portfolio of technologies that are either currently available or expected to be commercialised in coming decades, assuming appropriate and effective incentives are in place for their development, acquisition, deployment and diffusion and addressing related barriers.

But we need "substantial investment flows" and "effective technology transfer," meaning lots of money and getting the solutions to where they are needed. The longer we wait, the harder it is, because we need to begin to reverse that nasty increasing trendline, and the longer we wait, not only is it getting steeper, but because of the persistence of greenhouse gases, the stabilization level, and the attendant changes (such as temperature and sea level increases), will be higher. It looks from the chart like we have about ten years if we want things to stabilize at or near 2005 levels of greenhouse gases. If the CO2 peak comes after the 2010-2030 period, the resulting world will look very different from what we have now.

Update:

Surprise, surprise. The US representative tried to water the report down. More of the Bush/Cheney regime's attempts to make policy by denying reality. By contrast, the UN chief Ban Ki-moon calls for action.

September 17, 2007

The New York Times ran a good "personal history" piece on a woman who knows she inherited from her mother a copy of the tumor suppressor gene BRCA1 that predisposes her to breast and ovarian cancers at a young age (probably by the time she turns 40). It describes her struggle with the decision merely to monitor herself carefully or to commit to the best cure available against breast cancer: double mastectomy. It's an informed choice her generation will be the first to face.

Joan Lindner, 63, is a cancer survivor. Her daughter, by contrast, is one of a growing number of young women who call themselves previvors because they have learned early that they are genetically prone to breast cancer, and have the chance to act before it strikes. [...]

Parents who have fought cancer typically have no experience with the choices that confront their children, and guilt over being the biological source of the problem can color their advice. Siblings and cousins who carry the risk gene evangelize their own approach to managing it, while those who dodged its inheritance seem unqualified to judge.

The story is a sign of our changing relationship with our genetic inheritance -- not only the substance of the story, but the very fact that an entire family's genetic pedigree and relevant medical data, with their photos, was published as a front-page story in a major newspaper. Maybe it's the exhibitionism of the reality TV age dovetailing with the post-genome era: only one member of the pedigree declined to have his name and photo published. (Why didn't the NYT respect his wish for privacy and just leave him off the tree?) Not only do we know more than ever about our genetic makeup, we are sharing it.

Importantly, our ability to read (and publish) our genes is outpacing our philosophy of when to do so. Ultimately, the answer is simple: it's up to the individual. But those individuals will want to make an informed choice, and (as I've written many times) in a setting where about 3/4 of us believe in angels but only 1/4 believe in evolution, the infrastructure is not in place for people to be savvy consumers of genetic information. Add into the mix the self-interest of counseling companies, pharmaceutical companies, and insurance companies and you get a recipe for confusion and frustration.

How will we overcome it? There may emerge trustworthy companies to help you interpret whether new medical studies apply to you: for example, 23andMe was started recently by the wife of one of Google's founders (and with a substantial investment from Google itself) for just these ends. (Hm, and they're hiring...) But, I'm afraid people will always crave certainty and a quick fix, and that's not what most legitimate research will offer -- so, unfortunately, it's not time to sell short snake oil futures just yet.

And who gets to read your DNA? Your employer? Your insurance company? The government? New York Gov. Eliot Spitzer has been trying to expand DNA databasing to anyone convicted of a misdemeanor, and some states apparently collect DNA from anyone arrested (whether or not they are convicted). Will your DNA become a bit of personal information like your social security number -- putatively private, but in reality requested every time you fill out a form, apply for credit, visit your dentist?

Below these pragmatic concerns there exists a deeper question about humanity and free will. How "proactively" do we want to try to control our future, and to what degree should we realize that we may be able to lightly weight the dice, but in the end we can only really control our own attitudes toward what may come? Arlo Guthrie decided not to be tested for the copy of the gene that led to his father, Woody, dying of Huntington's disease, for which there is still no treatment. He recently passed the age at which his father died, and is still going strong without any sign of illness -- he said, "I spent the day talking to my dad about it, as it were [...] I said, 'All right, there's progress. And if my kids live a day older than I get to be, we're moving in the right direction, anyway.' "

September 11, 2007

You can learn a lot just by surfing. The American Society for Cell Biology (which I seem to be plugging a lot lately) has published a terrific set of lectures by some of the leading lights in the field. The full collection is at iBioSeminars, and they're all free.
Most are at a level suitable for advanced undergrads, but (as with any field) some speakers are clear enough that even someone with almost no background could follow easily. Martin Raff is one of my favorite communicators: here he is talking about how an organ -- or organism -- knows how big to grow:
Quicktime moved below the fold so it doesn't keep loading with the home page...

September 07, 2007

Cell biology in China is growing, and if the Chinese Society for Cell Biology (CSCB) can be considered "Exhibit A," the proof is strong indeed: CSCB now has nearly 3,000 members working at more than 200 universities and 40 institutes of the Chinese Academy of Sciences and Chinese Academy of Medical Sciences...

Government funding for research has risen dramatically in the last decade, as the Chinese economy has developed rapidly. From 1995 to 2004, Chinese science research funding increased from 0.6% to 1.23% of the gross domestic product. In 2006 the percentage rose to 1.4% (300 billion RMB Yuan, which is 22% higher than in 2005).

Given the pace of growth of the Chinese economy, that increase in the R&D-to-GDP ratio is amazing. And China is not alone. An NSF report last month says China, Singapore, Taiwan, and South Korea are all growing faster than the US:

From 1991 to 1995, R&D in Asia grew at a much faster annual rate (7.9%) than in the EU (3.4%) and in the United States (3.3%). After 1995, growth accelerated in Asia to an annual average of 8.7%, exceeding that of the EU (5.4%) and the 6.0% U.S. average.

China's annual rate of R&D growth from 1995 to 2003 (20%) exceeded that of all these other R&D performers, followed by Singapore's at 15%. Growth in Taiwan averaged 10% and in South Korea 7%

The rise of Asian research is fantastic for global science, and will give these growing countries a strong engine for continued economic growth. Unfortunately for us, it also means the US high-tech trade balance has turned negative. The good news is that we have a huge advantage in the American scientific infrastructure that's been built over the second half of the last century. If we spend money here instead of on foreign adventures, we will continue to lead. If not, not.

September 04, 2007

J. Craig Venter, one of the original competitors in the race to sequence the human genome, has sequenced and published his own DNA, the first time a single individual's genome has been sequenced.

In the New York Times, Nicholas Wade does a good job with the story, focusing on the original race between the academic consortium and Venter's then-company, Celera. The academic consortium won that race, and the first draft copy of the human genome sequence was public domain -- not privately owned, as Celera's version would have been. Venter left Celera and started a new institute (named for himself) and set out to sequence a single individual's DNA (his own). His success today is being portayed as a Return of the Jedi moment, with Venter in the hero's role. But to me, today's news is a big win for Venter, but an even bigger victory for public science.

Consider: Venter published the DNA sequence itself free, to the public, with no restrictions on its use. It's been deposited in the free, public DNA database at the government-funded National Center for Biotechnology Information, part of the NIH. He's going to publish, for free, his own medical records for researchers to compare his genetics and his health. And the paper itself was published in Public Library of Science (PLoS), an upstart journal begun a few years ago with the aim of overturning the subscription-only stranglehold of the Elsevier publishing empire, and hoping to become an Open Access journal of the same caliber as the subscription-only Science, Nature, and Cell.

As a result, you own his genome. You can read the original paper, free, the day it is published (today). If you're not in the field, you can read an editor's summary, written just for you, also free. There's a free interactive poster (PDF) for you to play with, and you can even access the raw data of the original shotgun sequencing reads, if you ever wanted to.

Venter gets the last word, but ultimately it's public science over privatized science that has won out. What's a real shame is that he had to raise money for this privately, because the NIH pocketbook is too tight to fund even a project of such monumental importance (and there were other issues too). Good for Venter for giving back to the public more than he was given.

August 27, 2007

Fifty years ago I was about to turn 15, it was 1957, and the central issue of our times was clearly seen to be the Cold War, the struggle with the Communist Soviet Union and its allies such as China. In retrospect, at least from the US perspective, that was probably accurate, although expanding civil rights and economic opportunity to those other than (straight) white men probably runs a close second. Fifty years from now, in 2057, when today's 15-year-olds are my age, when people look back at the beginning of the 21st Century, what do you think they are going to see as the central issue of our times? And how are they going to think we did?

I am willing to bet that it will not be the struggle with Islamic extremists, or even with terrorists generally, as the Bush/Cheney regime and its sycophants believe. Rather, it is much more likely to be the intertwined problems of the end of fossil fuels and global climate collapse. And depending on what we do in the next 5-10 years, they may be wondering why we didn't feel more of a sense of urgency, why we didn't do something while there was still time, why we threw so much money and effort at a crazy, endless war in the Middle East while the temperatures and sea levels rose around us.

While both major parties saw the struggle against communism as the central issue in the 1950's, it has been devastating to the cause of mitigating climate change that the GOP and its patrons have not only denied the urgency, but fought the effort tooth and nail for the first six years of the Bush presidency. But that began to change, as so much did, with Katrina, then with last summer's fires and heat waves, and now this summer's extreme weather events, all of which have cost many lives on all our coasts and the interior.

While Al Gore's "Inconvenient Truth" was seen as a political event, last night's Tom Brokaw special on the Discovery Channel was global warming 101 for the mainstream. A poll taken a year ago reported 70% of the public convinced that global warming is happening, an equal amount having become more convinced over the previous two years, with severe weather being a major factor in that change. This summer's severe rains and floods probably increased the number.

With a sufficient segment of the public now convinced theere is a problem, we sorely need real leadership on the issue. Based on the 1970's gasoline shortages and our experience here in Califonria with periodic shortages of water and electricity, I firmly believe that the public will respond favorably to clear direction and mandates for change. In parts of the country without such leadership many people do not do more because they believe that if the problem were real, the government would be doing something. Thus, we need first and foremost a clear statement that the problem is real, serious and must be addressed.

Second, people need to understand that while climate change cannot be arrested at this point, it can be mitigated, and that a little effort actually can go a long way. One of the most informative graphics in the Discovery Channel show depicted the carbon dioxide output of various activities and machines of a typical family as blocks of soot above the house. An amazing amount can be saved through conservation and efficiency around the home with negligible change in lifestyle. The California Flex Your Power website claims that if every household replaced one incandescent bulb with an energy-saving CFL bulb it would be the equivalent of taking a million cars off the road. (Flex Your Power is a model partnership of utilities, residents, businesses, institutions, government agencies and nonprofit organizations working to save energy formed during the 2001 energy crisis here. Its website has a wealth of ideas for saving energy.) In fact, addressing energy use in buildings and construction is at least as important as addressing conservation through better means of transportation, a point also made by the Discovery Channel special. Municipal, residential and business lighting is another area ripe for conservation. A fascinating article in theAugust 20, 2007 New Yorker discussed how improved outdoor lighting not only saves energy and allows more enjoyment of the night sky, but is actually safer as well. Tucson has long set an example in this area.

Finally, it is obvious that even as we conserve, we need to develop new technologies for building, transportation and power generation. Rather than costing jobs, this could become the next entrepreneurial frontier, if there were more incentives (such as fuel efficiency mandates, seed money and regulatory changes that mroe fairly internalized, rather than externalized, the costs of existing fuel sources).

Concern for the environment is one major area where young voters are disenchanted with the GOP. Along with the traqgic blunder that is Iraq, I believe that GOP denial of global warming and refusal to confront it as a major problem may prove the undoing of conservatism as an appealing ideology even to an extent in the ultra- conservative parts of the country. Certainly that would be the case if the Democratic Party leadership and candidates made addressing global warming and coping with declining supplies of fossil fuels through conservation and innovation a major part of their platform. Not to do so is to be wrong, colossally wrong, about the central issue of our time.

August 08, 2007

Somtimes, I question my own intentions. Do I really think it's in Americans' interest to pay me to do basic biology research, or do I just like getting paid? Is the NIH anything more than welfare for academics? When such moments strike, I like to turn for advice to a liberal luminary, an advocate of the power of Big Government doing big jobs for the common good. Someone like -- Newt Gingrich?

NIH funding has been flat since 2004, undermining the gains earned through the doubling of the budget and slowing the pace of progress in biomedical research. The Bush administration's proposed fiscal year 2008 budget would cut $329 million from last year's allocation of $28.6 billion. Biomedical inflation significantly compounds the impact of this reduction. This is exactly the wrong course for the country. Investment in the NIH should be expanded, not cut.

[...]

The National Institutes of Health Reform Act, approved by Congress in 2006, contained the authorization of an increase of 8 percent for the agency in 2008. The House Appropriations Committee vote on June 7 calling for a 2.6 percent increase for NIH does not go far enough. The House, Senate and the Bush administration should follow the 8 percent increase authorization, and make a choice now to secure longer, healthier lives for Americans with this as the benchmark for future years.

Those paragraphs, emphases mine, are from an op-ed Gingrich co-authored in the June 24 San Francisco Chronicle. As I recently posted, the current Senate and House plans increase the NIH budget by only 3.5%, compared to an inflation rate in the life sciences of 3.7% (detailed numbers here). The current plans also shift funding obligations around within NIH in a way that leaves most Institutes with increases of less than 2.5%, a stunning real dollar cut relative to inflation. At this point, let me stop and ask, what upside-down, ass-backwards planet am I living on when Gingrich advocates government spending on medical research while the Democratic Congress wants to starve it out?

The survey, which they received in May, asks their views about funding for NIH, CDC, and science education; American health care coverage and Medicare; and stem cell research. They can complete it by mail, fax, email, or on-line.

There is no excuse for any Congressperson to refuse to let their constituents know where they stand -- and to let us hold them accountable if their words are not backed up by actions.

July 17, 2007

Are Congressional Democrats really going to support stem cell research, or were stem cells simply a political device for the campaign trail?

We have seen that stem cell research is a useful political wedge to separate fundamentalist candidates, beholden to the extreme religious right, from an electorate of mainstream Republican voters (who support stem cell research). Democrats have done a great job stumping on stem cells and using legislation sure to be vetoed as a means to get incumbent Republicans on record voting against the publicly popular research.

But their policy action so far is disappointingly mixed. Democrats have continued to champion federal funding of stem cell research as a legislative matter -- that is, they have passed legislation aimed at reversing Bush's directive to the NIH and thereby freeing up federal money for the research. (A similar bill was also passed by the Republican-controlled House in May 2005 and the Republican-controlled Senate in September 2006.) However, when it comes to appropriating funding that would pay for that research, the current budget bills show a meager allocation for NIH, on par with the 2004-2006 budgets set by Republicans.